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Using Microwell-seq, we analyzed more than 500,000 single cells covering all major Xenopus tissues to construct the first Xenopus cell landscape to date. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. A comparison of larval and adult erythrocytes revealed larval and adult-specific hemoglobin subtypes and a cluster of erythrocytes containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibited both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism in metamorphosis. Our study provides a comprehensive resource for research on Xenopus developmental biology.

The rapid development of high-throughput single-cell RNA sequencing technology offers a good opportunity to dissect cell heterogeneity of animals. A large number of organism-wide single-cell atlases have been constructed for vertebrates such asHomo sapiens,Macaca fascicularis,Mus musculusandDanio rerio. However, an intermediate taxon that links mammals to vertebrates of more ancient origin is still lacking. Here, we construct the firstXenopuscell landscape to date, including larval and adult organs. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. The comparison of larval and adult erythrocytes identifies stage-specific hemoglobin subtypes, as well as a common type of cluster containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibits both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism during metamorphosis. Overall, our study provides a large-scale resource for research onXenopusmetamorphosis and adult organs.